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NAME¶
LogolExec - Program to parse a logol grammar and search pattern in a sequence.
INSTALLATION¶
Logol requires the Cassiopee Ruby gem. To install it run:
gem install cassiopee
CONFIGURATION¶
LogolExec use a default configuration file in /etc/logol/logol.properties. It
is possible to specify a different configuration file via command-line.
Temporary and results directory must be writable by the user.
By default, /var/lib/logol/results contains generated results and /tmp is used
at temporary directory.
.PP
OPTIONS¶
Minimum arguments are -m for logol model or -g for logol grammar, and -s for
input sequence
MAIN OPTIONS¶
- -h
-
display the list of commands.
- -v
-
get version
- -conf
-
specify configuration file
- -s
-
sequence file to analyse.
- -g
-
grammar file to analyse
- -m
-
model file to analyse
- -check
-
check a grammar, no execution. Requires -g
- -dna
-
analyse dna, is default
- -rna
-
analyse rna
- -protein
-
analyse protein
- -max
-
maximum returned solutions
- -all
-
analyse both directions of the sequence
- -output
-
output file name, must be unique
OTHER OPTIONS¶
- -sequenceID
-
position of sequence in bank
- -uid
-
Use a defined identifier for the query
- -lmax
-
maximum length of a variable
- -maxspacer
-
maximum size of a spacer
- -offset
-
Offset value to add to positions
- -start
-
Start position on sequence
- -end
-
End position on sequence
- -noclean
-
Do not delete created files after treatment (for debug)
- -enabledups
-
enable duplicate result matches. By default only keep singletons
- -filter
-
Type of filter when enabledups is not enabled. Allowed types are
exact(default),local,local0,global.
- -lmin
-
minimum length of a variable (to speedup parsing)
- -c
-
maximum size of a match (to speedup parsing)
- -maxres
-
maximum result size of a match (to speedup parsing)
AUTHOR¶
Olivier Sallou (olivier.sallou (at) irisa.fr)
